I'm not a programmer, but as far as I understand the system was not designed with alternate skins in mind (as mentioned before), so it does require a bit of work on the UI and under the hood, so I'm afraid this feature is not a priority.

You've mentioned it can't be used for quest/script units, but that should be different from proper faction.

So, to sum it up, Amplitude

• releases hero ship skin as part of Digital Deluxe edition and Craver fleet skin, as part of preorder bonus;
• releases even more skins as community DLC reward;
• claims system was not designed with skins in mind (can't be applied to AI players)

That sounds like a huge oversight.

Again I raise the point, if it's difficult to hard code into the game, make a series of alternative skin mods and release them on the worshop. Then you can even have the skins used by the AI. This would take some time, but would't require any system overhauls 

I had not yet joined Amplitude back then, so I can not speak to how the Alternate Skin system came to be implemented as it is, but given some of the problems I've seen reported with the alternative skins, I have come to realize that the system is more complicated than I believed before.

I'm sorry to hear our priorities are mysterious to some people, though. In the recent months, our top priority was the collaboration with NGD and ensuring that they are in the best position to do a great job with their work on Endless Space 2. Nonetheless, we are closely following the forums and will do our best to answer as many concerns as possible, and will talk more about this before the release of the expansion.

I am hopefully that this feature will become part of the base game before too much time has passed. I am happy to hear that we are on the radar. 

I definitely think this could be possible knowing how ship skins are applied.

I agree. I would love to have different fleet skins for the AI. Going up against a Mavros fleet would be awesome!